This data set was then expanded to cover papers published since 1995 (to August 2008) or those that were missed in the original set of analyses. Literature searches used diverse online databases-Carnivore Ecology & Conservation, Google Scholar, ScienceDirect, Scopus, the online catalog of the University of Jena/Provincial Library of Thuringia, Web of Science, Wiley InterScience and Zoological Record-using the search terms phylogen* or taxonom* or systemat* or cladistic* or clado* or classif* or morpholo* or crani* or bone or character or structu* in combination with the scientific or common names of each carnivore family. Secondary searches excluded publications including the keywords DNA or parasit* or molecul* or prädato* or genet* or mitoch*.
To counteract problems associated with data duplication among source trees and source trees of poor quality (see [29 (link)]), all source trees were subjected to the selection protocol outlined in Bininda-Emonds et al. [99 ] and excluded for one or more of the following reasons:
1. A publication date before 1970 so as to favor newer source trees based on more comprehensive data sets and analyzed using robust phylogenetic algorithms.
2. Insufficient information in the paper as to the data source underlying the source trees (for example, [100 (link)-105 (link)]).
3. Trees where characters were merely mapped onto an existing phylogeny unless it was explicitly mentioned that the characters were entirely congruent with the phylogeny (thereby representing independent support for it).
4. Papers lacking trees entirely and where the text was insufficient to accurately reconstruct the pattern of relationships implied for a source tree.
5. All molecular trees based on DNA sequence data that we were able to obtain separately (see below).
Where a publication contained more than one source tree, all independent source trees were identified using the protocols outlined in [99 ,106 (link)]. For non-independent source trees in the same publication, the preferred tree was the consensus of these trees in the first instance, followed by the most taxonomically complete tree or that explicitly preferred and justified by the authors. If none of these options were available, all source trees were coded and included in the main analysis; no mini-supertrees were made (contra [99 ]).
A total of 114 trees were thus obtained, 86.3% of which were also used by Bininda-Emonds et al. [1 (link)]. (The much smaller number compared with the original study (274) is because the original, nested supertree analysis meant that the same source tree could simultaneously contribute to more than one supertree analysis.) Of the original source trees, 27 were excluded for the reasons outlined above.
As a final step, the taxonomy of the source trees was standardized to the list of species names found in Wozencraft [14 ] using the Perl script synonoTree.pl v2.2 [99 ]. Taxon names that did not belong to crown group Carnivora were deleted outright, although the source trees containing them were held to be rooted (see below). For higher-level taxon names, the name-bearing type species was substituted wherever possible (for example, Canis lupus for Canidae); otherwise, the taxon was deleted from the source tree as was also the case for ambiguous names (for example, dog). synonoTree also accounts for species that occur more than once on a given tree through the synonymization process by outputting all possible permutations of the tree with the taxa represented once in all possible positions and combinations; these non-independent trees could later be down-weighted appropriately. Including permutations that arose because of the synonymization process, a total of 241 literature trees were obtained.